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<title>viewMultiTCW</title>
<h2>Instructions</h2>
Terminology:
<ul>
<li><i>Sequence:</i> A protein sequence from one of the sTCW projects that were combined into the mTCW project.  
<li><i>Cluster:</i> A cluster of sequences created by one of the clustering methods. There may be more
than one set of clusters in the database; see Methods in the Overview for a list of
the methods used to build the clusters.
<li><i>Species:</i> The multiTCW database was created from one or more singleTCW databases,
where each one is referred to as a species within the multiTCW.
</ul>
A few general rules:
<ol>
<li>
Selecting a label on the left results in a table, menu or sequence being displayed on
the right.
<li>There are two types of tables: Clusters and Sequences, where Sequences may be members of a cluster.
<li>Columns can be changed for all tables using the <b>Select Columns</b> button below the table. 
<li>Columns can be sorted by clicking the column heading, and can be moved by dragging them.
<li>The columns viewed are saved (i.e. the next time you view the table, you will see the same columns). However,
the sorting and dragging of columns is not saved.
<li>Rows are selected by clicking, and multiple rows can be selected using ctrl-click or shift-click. 
</li>
</ol>
</ol>
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<b>&gt;All Clusters</b> - A table of all clusters in the database. 
<ul>
<li>To view the members of a cluster, select the row and then "View Selected Cluster". 
<li>The MUSCLE alignment of the member of a cluster (not available from the web) 
and the pairwise alignments can be computed and displayed.
</ul>

<b>&gt;All Sequences</b> - A table of all peptide sequences in the database (note, if
a nucleotide sequence was not translated by ESTscan, it will not be shown).
<ul>
<li>To view sequence details, select <b>View Details</b>.
<li>To view the clusters that a sequence is in, select <b>View Clusters</b>;
note that a sequence may not be in any cluster. 
</ul>

<b>&gt;Filter Clusters</b> - Search filters for clusters.
<ul>
<li>View clusters that have sequences from a selected set of
species.
<li>Query on Cluster ID, cluster method, and annotation keywords. 
</ul>

<b>&gt;Filter Sequences</b> - Search filters for sequences.
<ul>
<li>Sequence ID is the only filter currently available. 
</ul>

<b>&gt;Results</b> - List of prior filter search results.

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